GERMS platform for Microbial Genomics

Principle Investigator

GERMS wants to be your genomics partner for the investigation of microbial diseases in Singapore.

GERMS is a GIS platform that provides comprehensive genomics solutions for studying the role of microbes in human health and diseases. The GERMS platform integrates GIS’ extensive experimental and analytical expertise in the study of viruses, bacteria, fungi, parasites and microbiomes. The platform supports everything from small to large studies involving genome sequencing, transcriptomics, functional genomics, metagenomics as well as custom applications. We partner with research and clinical groups around the world to study health and infection in single patients to whole hospitals, communities and beyond. Some recent examples of GERMS-enabled projects include:

We combined genomics with traditional epidemiology during a Group A Streptococcus outbreak in a local hospital. Together these identified that there was a single strain causing an outbreak in a particular ward but not throughout the hospital. In the absence of genomics, the infection control team was considering hospital-wide antibiotic prophylaxis. However, the higher resolution of whole genome sequencing enabled a targeted intervention to control the outbreak, saving the hospital money and saving many patients from unnecessary antibiotic treatment. Importantly, we helped perform the genome sequencing and analysis on a time scale fast enough to impact infection control interventions.
PMID: 29739475

Metagenomics: Can skin microbes predispose you to eczema?

with A*STAR’s Institute of Medical Biology, Singapore

Eczema or Atopic Dermatitis (AD) is a common, recurrent, inflammatory skin disease affecting nearly 1 in 5 individuals globally. The skin microbiome of eczema patients with apparently normal, inter-flare skin was dominated by a host of opportunistic pathogens. We showed that many of these opportunistic pathogens were inhibited S. aureus colonization, suggesting that there was bacterial competition and that S. aureus was in effect “keeping the peace” in the non-flare state. On the flip side, depleted bacteria had metabolic, antibiotic and anti-inflammatory properties that suggest that they may have a protective role in normal individuals. Immune challenge assays with keratinocytes and dendritic cells further confirmed that these AD-associated bacteria have distinct functional roles.
PMID: 27562258

Macromolecular therapeutics for drug resistant superbugs

with A*STAR’s Institute of Bioengineering and Nanotechnology, Singapore & the International Business Machine, USA, University of North Dakota’s School of Medicine and Health Sciences, USA and the First Affiliated Hospital of Zhejiang University’s College of Medicine, China

Superbugs that are resistant to antibiotics are a serious health threat. The research community is trying to develop alternatives to antibiotics using synthetic polymers. These biodegradable synthetic macromolecules have broad-spectrum antimicrobial activity in mice, a unique killing mechanism and no toxicity in animal models. To determine whether the bacteria will develop any resistance to the polymer, the team collaborated with GERMS to perform genomic analysis. We found that the bacteria did not show any resistance development even after multiple treatments with the polymer. Their new polymer material holds promise to be developed into an antimicrobial drug to treat patients with antibiotic-resistant infections.
PMID: 29500445

Outbreak of Zika in Singapore

with Singaporean Ministry of Health, TTSH, Environmental Health Institute, Duke-National University of Singapore, A*STAR Bioinformatics Institute and Oxford University Clinical Research Unit, Vietnam & many more collaborators from Singaporean hospitals & agencies

There was a Zika outbreak in Singapore in 2016. The major concern was whether this outbreak was imported from Brazil or elsewhere in the Americas, because that was where Zika was associated with birth defects (microcephaly) after mothers became infected. To answer this question, we used genomics, or sequencing of the viral RNA for Zika virus. We adapted expertise we had in doing genomics on Dengue to study Zika samples from Singapore. We found that the Zika outbreak in Singapore was due to a strain of Zika that was from Southeast Asia - and not from Brazil or elsewhere in the Americas. This helped to provide information to the public health agencies for communicating the risks of Zika infection as well as to target mosquito control in Singapore, a key measure important for both Dengue and Zika control.
PMID: 28527892

16S: Microbiome development in childhood diarrhea

with Oxford University Clinical Research Unit in Vietnam

We are becoming increasingly aware of the importance of the role of the gut microbiome on the effects on health and disease later in life. We collaborated with the Oxford University Clinical Research Unit in Vietnam to investigate the effect of viral or bacterial diarrhea on young children in this region, to further our understanding of bacteria in the gut and how these bacteria influence health.
PMID: 28767339

Other publications from GERMS members, since 2016:

Chen Lab

A Sub-population of Group A Streptococcus Elicits a Population-wide Production of Bacteriocins to Establish Dominance in the Host. Cell Host Microbe. 2018 PMID: 29544095

The epidemiology and transmission of methicillin-resistant Staphylococcus aureus in the community in Singapore: study protocol for a longitudinal household study. BMC Infect Dis. 2017 PMID:29020940 [study protocol]